feat: add index option to case import

varfish_cli/cli/importer/__init__.py

@@ -133,6 +133,13 @@ def cli_caseimportinfo_create(
             help="The genome build (GRCh37/GRCh38) of this case, defaults to GRCh37.",
         ),
     ] = GenomeBuild.GRCH37.value,
+    index: typing.Annotated[
+        str,
+        typer.Option(
+            "--index",
+            help="Name of the index case in the pedigree, defaults to the first case.",
+        ),
+    ] = None,
 ):
     logger.info("Creating CaseImportInfo object...")
     common_options: CommonOptions = ctx.obj
@@ -145,6 +152,7 @@ def cli_caseimportinfo_create(
             force_fresh=force_fresh,
             resubmit=resubmit,
             project_uuid=project_uuid,
+            index=index,
         ),
         common_options=common_options,
     )

varfish_cli/cli/importer/create.py

@@ -279,6 +279,7 @@ class CaseImportOptions(pydantic.BaseModel):
     resubmit: bool
     force_fresh: bool
     case_name_suffix: str
+    index: typing.Union[str, None]
 
 
 class CaseImporter:
@@ -315,6 +316,7 @@ def __init__(self, options: CaseImportOptions, common_options: CommonOptions):
 
         #: The pedigree members.
         self.pedigree: typing.List[PedigreeMember] = None
+        self.index: typing.Union[str, None] = options.index
 
     def _log_exception(self, e):
         logger.exception(e, exc_info=self.common_options.verbose)
@@ -519,7 +521,9 @@ def strip_suffix(x):
             return x
 
         name, self.pedigree = self._load_pedigree()
-        index = self.pedigree[0].name
+        if self.index and self.index not in {member.name for member in self.pedigree}:
+            raise ValueError(f"Specified index case '{self.index}' not found in pedigree")
+        index = self.index or self.pedigree[0].name
         name = strip_suffix(name)
 
         self._check_genotypes()